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| Cluster | Chromosome | Count | Expected | log2FE | Adjusted.pvalue |
|---|---|---|---|---|---|
| Cluster007 | Chr4 | 99 | 23.55 | 2.07 | 4.772e-35 |
| Cluster023 | Chr4 | 40 | 6.11 | 2.71 | 2.707e-23 |
| Cluster026 | Chr4 | 20 | 5.03 | 1.99 | 1.810e-06 |
| Cluster135 | Chr4 | 9 | 0.99 | 3.19 | 6.997e-07 |
| Cluster086 | Chr12 | 7 | 0.42 | 4.05 | 3.447e-06 |
| Cluster057 | Chr23 | 6 | 0.69 | 3.13 | 1.637e-03 |
Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).
| Cluster | Freq | |
|---|---|---|
| 7 | Cluster007 | 96 |
| 23 | Cluster023 | 30 |
| 26 | Cluster026 | 18 |
| 2 | Cluster002 | 10 |
| 135 | Cluster135 | 9 |
| 24 | Cluster024 | 5 |
Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).
The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.
| Cluster | Category | Count | Expected | log2FE | pvalue | adjusted.pvalue |
|---|---|---|---|---|---|---|
| Cluster007 | Chr4ZnF | 96 | 27.28 | 1.82 | 4.048e-25 | 2.429e-24 |
Table showing clusters with significant enrichments (adjusted p-value < 0.05).
There are 9 clusters with more than 8 genes on chr 4. Need a colour palette for 9 clusters.
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Histogram showing the distribution of genes in clusters 7, 23, 26 and 135.
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Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).
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Line graph showing the distribution of ZnF and NLR genes on chromosome 4 (binwidth = 5 Mb).
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## Chr1-29279647-29885073
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## Chr4-40461327-40771283
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## Chr4-50661962-50742100
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## Chr4-53865601-53897347
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## Chr4-59585793-59894990
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## Chr4-64684113-65167069
## Chr4-65983752-66208723
## Chr4-69945188-70379008
## Chr6-39293241-39510839
## Chr7-72096634-72338230
## Chr7-73590418-73606060
## Chr8-16573954-16576906
## Chr9-7477783-8100425
## Chr10-18994837-19609041
## Chr12-2412104-2635423
## Chr14-11072281-11303764
## Chr14-33251312-33594799
## Chr15-15378107-15524111
## Chr16-11694674-11888570
## Chr17-46839113-47219486
## Chr19-20156555-20400250
## Chr19-40763348-41319041
## Chr20-3272730-3309124
## Chr22-895552-1103977
## Chr22-2126341-2194312
## Chr22-28909098-29133881
## Chr23-35954141-36004832
## Chr23-37221300-37504077
## Chr23-40277439-40573494
## Chr24-192921-523267
## Chr24-3447094-4408464
## Chr24-6078572-6641761
## Chr24-29485795-30192806
## Chr25-12951696-13285349
## Chr25-34607134-34628832
## Chr25-34843668-35322690
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Kernel density estimate of Pearson coefficients between paralogous gene pairs
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## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] R2HTML_2.3.2 rgl_0.98.1
## [3] qvalue_2.6.0 genefilter_1.56.0
## [5] DESeq2_1.14.1 SummarizedExperiment_1.4.0
## [7] htmlTable_1.9 biomaRt_2.30.0
## [9] Rgraphviz_2.18.0 gridExtra_2.2.1
## [11] topGO_2.26.0 SparseM_1.77
## [13] GO.db_3.4.0 graph_1.52.0
## [15] cba_0.2-19 proxy_0.4-16
## [17] RColorBrewer_1.1-2 plyr_1.8.4
## [19] GenomicFeatures_1.26.4 AnnotationDbi_1.36.2
## [21] Biobase_2.34.0 GenomicRanges_1.26.4
## [23] GenomeInfoDb_1.10.3 IRanges_2.8.2
## [25] S4Vectors_0.12.2 scales_0.4.1
## [27] reshape2_1.4.2 ggbio_1.22.4
## [29] BiocGenerics_0.20.0 ggplot2_2.2.1
## [31] rprojroot_1.2 knitr_1.16
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 matrixStats_0.52.2
## [3] bit64_0.9-7 httr_1.2.1
## [5] tools_3.3.1 backports_1.1.0
## [7] R6_2.2.2 rpart_4.1-11
## [9] Hmisc_4.0-3 DBI_0.7
## [11] lazyeval_0.2.0 colorspace_1.3-2
## [13] nnet_7.3-12 GGally_1.3.1
## [15] bit_1.1-12 labeling_0.3
## [17] rtracklayer_1.34.2 checkmate_1.8.2
## [19] RBGL_1.50.0 stringr_1.2.0
## [21] digest_0.6.12 Rsamtools_1.26.2
## [23] foreign_0.8-69 rmarkdown_1.6
## [25] XVector_0.14.1 base64enc_0.1-3
## [27] dichromat_2.0-0 pkgconfig_2.0.1
## [29] htmltools_0.3.6 highr_0.6
## [31] ensembldb_1.6.2 BSgenome_1.42.0
## [33] htmlwidgets_0.8 rlang_0.1.1
## [35] RSQLite_2.0 BiocInstaller_1.24.0
## [37] shiny_1.0.3 jsonlite_1.5
## [39] BiocParallel_1.8.2 acepack_1.4.1
## [41] VariantAnnotation_1.20.3 RCurl_1.95-4.8
## [43] magrittr_1.5 Formula_1.2-1
## [45] Matrix_1.2-10 Rcpp_0.12.11
## [47] munsell_0.4.3 stringi_1.1.5
## [49] yaml_2.1.14 zlibbioc_1.20.0
## [51] AnnotationHub_2.6.5 blob_1.1.0
## [53] lattice_0.20-35 Biostrings_2.42.1
## [55] splines_3.3.1 annotate_1.52.1
## [57] locfit_1.5-9.1 geneplotter_1.52.0
## [59] XML_3.98-1.9 evaluate_0.10.1
## [61] biovizBase_1.22.0 latticeExtra_0.6-28
## [63] rnaseqVis_0.0.0.9001 data.table_1.10.4
## [65] httpuv_1.3.3 gtable_0.2.0
## [67] reshape_0.8.6 mime_0.5
## [69] xtable_1.8-2 survival_2.41-3
## [71] tibble_1.3.3 OrganismDbi_1.16.0
## [73] GenomicAlignments_1.10.1 memoise_1.1.0
## [75] cluster_2.0.6 interactiveDisplayBase_1.12.0